Hi everyone,
I am trying to install Amber22 on the Frontier supercomputer at Oak Ridge National Lab. The compute nodes are composed of AMD Optimized 3rd Gen EPYC CPUs and AMD MI250X GPUs. I can install AmberTools 23/Amber22 without GPU support without any problems (and the install passes the test suite). However, I run into problems when trying to install with GPU support.
I’m following the AMD recipe found here: https://ambermd.org/GPUSupport.php
When I try to install, I first get an error message related to nab2c, mpinab2c, and rule_parse (they aren’t being built). It is our understanding nab2c is no longer part of AmberTools, so I tried dropping it from the install. I did this by editing line #6 of amber22_src/cmake/RunnablePrograms.cmake:
# original
#set(EXECUTABLES_TO_IMPORT ucpp utilMakeHelp nab2c mpinab2c rule_parse)
# dropping references to nab2c, mpiab2c rule_parse
set(EXECUTABLES_TO_IMPORT ucpp utilMakeHelp)
(if this is a bad idea, please let me know)
When I do this, the install makes more progress, but then I run into library errors. Here’s the first error (which consequently cascades into additional library error until the install fails):
Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /my_dir/amber22_src/build/amber/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_c11a7/fast && /usr/bin/gmake -f CMakeFiles/cmTC_c11a7.dir/build.make CMakeFiles/cmTC_c11a7.dir/build
gmake[1]: Entering directory '/my_dir/amber22_src/build/amber/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_c11a7.dir/src.c.o
/opt/cray/pe/gcc/12.2.0/bin/gcc -DCMAKE_HAVE_LIBC_PTHREAD -O3 -std=gnu99 -o CMakeFiles/cmTC_c11a7.dir/src.c.o -c /my_dir /amber22_src/build/amber/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_c11a7
/autofs/nccs-svm1_sw/frontier/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/cmake-3.23.2-4r4mpiba7cwdw2hlakh5i7tchi64s3qd/bin/cmake -E cmake_link_script CMakeFiles/cmTC_c11a7.dir/link.txt --verbose=1
/opt/cray/pe/gcc/12.2.0/bin/gcc -O3 CMakeFiles/cmTC_c11a7.dir/src.c.o -o cmTC_c11a7
/usr/bin/ld: CMakeFiles/cmTC_c11a7.dir/src.c.o: in function `main':
src.c:(.text.startup+0x13): undefined reference to `pthread_create'
/usr/bin/ld: src.c:(.text.startup+0x1d): undefined reference to `pthread_detach'
/usr/bin/ld: src.c:(.text.startup+0x27): undefined reference to `pthread_cancel'
/usr/bin/ld: src.c:(.text.startup+0x33): undefined reference to `pthread_join'
collect2: error: ld returned 1 exit status
Here’s my module load (providing some info on the environment):
craype-x86-trento
libfabric/1.15.2.0
craype-network-ofi
perftools-base/22.12.0
xpmem/2.5.2-2.4_3.45__gd0f7936.shasta
cray-pmi/6.1.8
gcc/12.2.0
craype/2.7.19
cray-dsmml/0.2.2
cray-mpich/8.1.23
cray-libsci/22.12.1.1
PrgEnv-gnu/8.3.3
darshan-runtime/3.4.0
hsi/default
DefApps/default
rocm/5.3.0
cmake/3.23.2
boost/1.79.0
zlib/1.2.11
bzip2/1.0.8
Has anyone else run into these problems installing Amber22 on systems with AMD GPUs? (or, has anyone recently had success with an AMD GPU installation)?
Please let me know whatever additional information I can provide that would be useful.
Thanks very much for any assistance!
Derek
Derek M. Shore, Ph.D.
Lecturer of Physiology and Biophysics
Scientific Computing Technology Engineer
Institute for Computational Biomedicine
Weill Cornell Medicine
Department of Physiology and Biophysics
1300 York Avenue, Room LC501A
New York, NY 10065
T: 212-746-6386
des2037.med.cornell.edu<mailto:des2037.med.cornell.edu>
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Received on Mon Jun 05 2023 - 09:30:02 PDT
